Dependancies and installation

Get the pipeline

$ git clone https://forgemia.inra.fr/umr-gdec/magatt.git

Dependencies - Conda

We recommend to build the environment using conda (developped with miniconda 3, conda 4.9.2 ) with the file environment.yml:

$ conda env create -f environment.yml -n magatt

Once created, you can activate the environment with:

$ conda activate magatt

All the dependancies installed in the conda env are listed below.

  • Snakemake : >=5.5.2

  • Python: 3.5

  • Biopython: 1.68

  • numpy: 1.15

  • pandas: 0.23

  • pysam: 0.15

  • Bedtools: 2.27

  • Blat: 36

  • Exonerate (fastavalidcds): 2.4.0

  • GenomeTools: 1.5.9

  • gffread: 0.9.11

  • GMAP: 2018-05-11

  • NCBI-blast (BLAST+): 2.6

  • Samtools: 1.9

  • BWA: 0.7